Variant report

Variant	rs28562980
Chromosome Location	chr4:3881655-3881656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3875544..3878977-chr4:3880853..3884345,4	MCF-7	breast:
2	chr4:3766377..3769370-chr4:3879934..3883138,3	K562	blood:
3	chr4:3867932..3870824-chr4:3880494..3883548,4	K562	blood:
4	chr4:3867255..3869432-chr4:3880872..3883548,2	K562	blood:

Variant related genes	Relation type
ENSG00000184160	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10022368	1.00[EUR][1000 genomes]
rs28374089	1.00[EUR][1000 genomes]
rs28385450	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402862	1.00[EUR][1000 genomes]
rs28421489	1.00[EUR][1000 genomes]
rs28431790	1.00[EUR][1000 genomes]
rs28535983	1.00[EUR][1000 genomes]
rs28579405	1.00[EUR][1000 genomes]
rs28609277	1.00[EUR][1000 genomes]
rs28700069	1.00[EUR][1000 genomes]
rs28729567	1.00[EUR][1000 genomes]
rs28854823	1.00[EUR][1000 genomes]
rs4075847	1.00[EUR][1000 genomes]
rs57505858	1.00[EUR][1000 genomes]
rs60592007	1.00[EUR][1000 genomes]
rs73074510	1.00[EUR][1000 genomes]
rs73082783	1.00[EUR][1000 genomes]
rs7436872	1.00[EUR][1000 genomes]
rs7436914	1.00[EUR][1000 genomes]
rs7438935	1.00[EUR][1000 genomes]
rs7441756	1.00[EUR][1000 genomes]
rs7441835	1.00[EUR][1000 genomes]
rs7442616	1.00[EUR][1000 genomes]
rs7665373	1.00[EUR][1000 genomes]
rs7672824	1.00[EUR][1000 genomes]
rs7684356	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933265	chr4:3392824-4283640	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv2757918	chr4:3394344-4350986	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2759219	chr4:3394344-4350986	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv878471	chr4:3413209-3884998	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	esv1816543	chr4:3414654-3942867	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1011554	chr4:3436478-3975772	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv537002	chr4:3436478-3975772	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv998670	chr4:3453787-3909535	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv432549	chr4:3487321-3975048	Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv878508	chr4:3737883-3884998	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	esv2763838	chr4:3874896-4199043	Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv1005868	chr4:3877778-4167133	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	esv2760820	chr4:3877790-4176629	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv998727	chr4:3879606-4186049	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3880400-3882200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:3880600-3881800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr4:3880800-3882000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:3880800-3882400	Weak transcription	Right Atrium	heart
5	chr4:3881000-3882000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:3881000-3882000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
7	chr4:3881000-3882200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:3881000-3882200	Bivalent Enhancer	Fetal Thymus	thymus
9	chr4:3881200-3881800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
10	chr4:3881200-3881800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr4:3881200-3881800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr4:3881200-3882000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:3881200-3882000	Bivalent Enhancer	Left Ventricle	heart
14	chr4:3881200-3882000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
15	chr4:3881200-3882000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
16	chr4:3881200-3882200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr4:3881200-3882200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr4:3881200-3882400	Bivalent Enhancer	Fetal Brain Male	brain
19	chr4:3881200-3882400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr4:3881200-3882600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:3881200-3882800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:3881400-3881800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:3881400-3881800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr4:3881400-3881800	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr4:3881400-3881800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr4:3881400-3882000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
27	chr4:3881400-3882000	Bivalent Enhancer	Brain Germinal Matrix	brain
28	chr4:3881400-3882400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr4:3881400-3882400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
30	chr4:3881400-3882400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:3881400-3882400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:3881400-3882400	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr4:3881400-3882600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:3881600-3881800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
35	chr4:3881600-3881800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
36	chr4:3881600-3881800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
37	chr4:3881600-3881800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr4:3881600-3881800	Weak transcription	Spleen	Spleen
39	chr4:3881600-3882000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
40	chr4:3881600-3882000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:3881600-3882200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr4:3881600-3882200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr4:3881600-3882200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:3881600-3882200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:3881600-3882200	Bivalent Enhancer	Adipose Nuclei	Adipose
46	chr4:3881600-3882200	Enhancers	HSMM	muscle
47	chr4:3881600-3882400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:3881600-3882400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:3881600-3882800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle

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